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xcmsRaw - error #683
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I have no experience with Waters software - but the file you exported can indeed not be read/imported with |
Or, leave netCDF behind and go straight to export/conversion to mzML ? Also, try to avoid the ancient xcms classes xcmsRaw and xcmsSet. They are not maintained anymore, in favour of the new xcms3 interface described in the vignette http://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html Yours, Steffen |
Johaness and Steffen, A little bit late but thanks for your response. I tried Proteowizard but it is not "seeing" the files. I am running R version 4.3.1 and cannot make mzR to work on the data from msdata. Any suggestion? Finally, as a new user of metabolomic data and potentially xcms, I found myself going through multiple vignettes/versions - in the end I figured out what was going on ... Thanks |
Could you give more information about that instrument and data ? In the netCDF I see |
But, partly successful. I don't think it is the missing instrument that breaks xcms:
which looks weird. There are some scans:
and the last one looks broken, the NA is likely to throw off calculations like min/max. Yours, |
One more thing:
but you'd need to play with parameters to find peaks:
Yours, |
I am learning about hp-lc data using xcms and obtained an error message when I was trying to import a .cdf file using xcmsRaw. The file was generated in a Waters HP-LC. I am wondering whether I am exporting the data incorrectly or if there something else that I have to be aware of. I am attaching the file just in case.
Many thanks for any help that you can provide.
Carla
Export_2023_07_241045.cdf.zip
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